Variant report

Variant	rs4931513
Chromosome Location	chr12:31675229-31675230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10771826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10771830	0.89[EUR][1000 genomes]
rs10771831	0.86[EUR][1000 genomes]
rs10771833	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[EUR][1000 genomes]
rs10771834	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10771835	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10771837	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10843937	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs10843938	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs10843939	0.86[EUR][1000 genomes]
rs10843953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10843954	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10843957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10843962	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843966	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843968	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843969	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10843971	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10843972	0.83[EUR][1000 genomes]
rs11051417	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11051427	0.87[EUR][1000 genomes]
rs11051428	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11051440	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11051446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11051454	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11051461	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11051467	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11051472	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11051476	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1150948	0.88[ASN][1000 genomes]
rs1150949	0.95[ASN][1000 genomes]
rs12368987	0.84[EUR][1000 genomes]
rs12369701	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12371432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259360	0.95[ASN][1000 genomes]
rs1268747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560634	0.83[EUR][1000 genomes]
rs1677193	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap]
rs16918740	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1879385	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2163730	0.87[EUR][1000 genomes]
rs2351921	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2351922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2351923	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2892638	0.84[EUR][1000 genomes]
rs34498192	0.90[EUR][1000 genomes]
rs3741877	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs3741878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3803114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3850966	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3887250	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3898712	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4931499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4931511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931512	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61097018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61918606	0.86[EUR][1000 genomes]
rs61930275	0.84[EUR][1000 genomes]
rs6487990	0.84[EUR][1000 genomes]
rs6487991	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6487995	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7132688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136559	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7297507	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7297997	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs7299425	0.83[EUR][1000 genomes]
rs7300106	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs7301326	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7302695	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73080572	0.86[EUR][1000 genomes]
rs7308202	0.89[EUR][1000 genomes]
rs7311970	0.84[EUR][1000 genomes]
rs7313889	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs7314404	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs7314739	0.86[EUR][1000 genomes]
rs7960380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7963764	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7978277	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4931513	FLJ13224	cis	cerebellum	SCAN
rs4931513	YARS2	cis	cerebellum	SCAN
rs4931513	DENND5B	cis	cerebellum	SCAN
rs4931513	DENND5B	cis	parietal	SCAN
rs4931513	ERGIC2	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31667800-31675400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:31667800-31687600	Weak transcription	Pancreas	Pancrea
3	chr12:31669800-31677800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr12:31670000-31675400	Enhancers	Fetal Kidney	kidney
5	chr12:31670000-31675400	Enhancers	Fetal Lung	lung
6	chr12:31670000-31676400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:31670200-31676800	Enhancers	Fetal Heart	heart
8	chr12:31671000-31680200	Weak transcription	Right Atrium	heart
9	chr12:31671200-31675400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:31671400-31677600	Enhancers	GM12878-XiMat	blood
11	chr12:31671800-31677800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:31672000-31678600	Weak transcription	Left Ventricle	heart
13	chr12:31672200-31678400	Weak transcription	Adipose Nuclei	Adipose
14	chr12:31672200-31678600	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:31672200-31680000	Weak transcription	Right Ventricle	heart
16	chr12:31672400-31676000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr12:31672400-31676600	Enhancers	Hela-S3	cervix
18	chr12:31672400-31677200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:31672600-31675400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr12:31672600-31677600	Weak transcription	Brain Angular Gyrus	brain
21	chr12:31672600-31679000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:31672800-31677800	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr12:31672800-31681000	Weak transcription	Brain Anterior Caudate	brain
24	chr12:31673000-31675400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:31673000-31677200	Weak transcription	HSMMtube	muscle
26	chr12:31673000-31678000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr12:31673000-31678000	Weak transcription	Fetal Brain Female	brain
28	chr12:31673000-31684600	Weak transcription	Aorta	Aorta
29	chr12:31673000-31685200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr12:31673200-31679600	Weak transcription	Brain Substantia Nigra	brain
31	chr12:31673400-31675400	Weak transcription	Brain Germinal Matrix	brain
32	chr12:31673400-31676200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:31673400-31676800	Weak transcription	HSMM	muscle
34	chr12:31673400-31677600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:31673400-31677600	Weak transcription	HMEC	breast
36	chr12:31673400-31677800	Weak transcription	Primary B cells from cord blood	blood
37	chr12:31673400-31677800	Weak transcription	NHDF-Ad	bronchial
38	chr12:31673400-31681200	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:31673400-31681600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:31673400-31688400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:31673600-31675400	Enhancers	Primary B cells from peripheral blood	blood
42	chr12:31674000-31676800	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr12:31674200-31675600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:31674200-31676400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:31674600-31675400	Enhancers	Liver	Liver
46	chr12:31674600-31675400	Flanking Active TSS	A549	lung
47	chr12:31674600-31675800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:31674600-31675800	Enhancers	Colon Smooth Muscle	Colon
49	chr12:31674600-31675800	Enhancers	Fetal Intestine Large	intestine
50	chr12:31674600-31675800	Enhancers	Psoas Muscle	Psoas

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